Parser for the SWISS-PROT 38 format.
You probably want to use the variables 'record' (for a single record)
and 'format' (for a set of records).
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ID = Martel.Group("ID", Martel.Str("ID ")+ Std.dbid(Martel.W...
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AC = Martel.Group("AC", Martel.Str("AC ")+ Std.dbid(Martel.W...
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AC_block = Martel.Group("AC_block", Martel.Rep1(AC))
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DT_created = Martel.Group("DT_created", Martel.Str("DT ")+ T...
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DT_seq_update = Martel.Group("DT_seq_update", Martel.Re(r"DT ...
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DT_ann_update = Martel.Group("DT_ann_update", Martel.Re(r"DT ...
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DE = Martel.Group("DE", Martel.Str("DE ")+ Std.description(M...
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DE_block = Std.description_block(Martel.Group("DE_block", Mart...
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GN = Simple("GN", "gene_names")
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GN_block = Martel.Group("GN_block", Martel.Rep1(GN))
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OS = Simple("OS", "organism_species")
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OS_block = sprot38.OS_block
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OG = Simple("OG", "organelle")
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OG_block = sprot38.OG_block
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OC = Simple("OC", "organism_classification")
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OC_block = sprot38.OC_block
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RN = sprot38.RN
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RP = sprot38.RP
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RC = Simple("RC", "reference_comment")
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RC_block = sprot38.RC_block
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RX = sprot38.RX
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RA = Simple("RA", "reference_author")
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RA_block = sprot38.RA_block
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RT = Simple("RT", "reference_title")
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RT_block = sprot38.RT_block
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RL = Simple("RL", "reference_location")
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RL_block = sprot38.RL_block
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reference = Martel.Group("reference", RN+ RP+ Martel.Opt(RC_bl...
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CC_begin = Martel.Group("CC", Martel.Re("CC -!- ")+ Martel.T...
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CC = Martel.Group("CC", Martel.Re("CC ")+ Martel.ToEol("...
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single_comment = Martel.Group("comment", CC_begin+ Martel.Rep(...
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CC_copyright_begin = Martel.Group("CC_copyright_begin", Martel...
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CC_copyright = Martel.Group("CC_copyright", Martel.Re("CC (?...
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CC_copyright_end = Martel.Group("CC_copyright_end", Martel.Re(...
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bogus_DR_group = Martel.Group("bogus_DR_block", Martel.Re(r"(?...
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comment = Martel.Group("comment_block", Martel.Rep(single_comm...
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_to_secondary_end = Martel.Re(r"([^.\R]|(?!.\R)\.)+")
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database_id = Std.dbxref_dbname(Martel.UntilSep("database_iden...
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primary_id = Std.dbxref_dbid(Martel.UntilSep("primary_identifi...
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secondary_id = Std.dbxref_dbid(Martel.Group("secondary_identif...
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real_DR_general = Std.dbxref(database_id+ Martel.Str("; ")+ pr...
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fast_DR_general = Std.fast_dbxref(real_DR_general, {"style": "...
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DR_general = Martel.FastFeature(fast_DR_general, "fast-sp-dbxr...
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real_DR_prosite = Std.dbxref(Std.dbxref_dbname(Martel.Group("d...
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fast_DR_prosite = Std.fast_dbxref(real_DR_prosite, {"style": "...
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DR_prosite = Martel.FastFeature(fast_DR_prosite, "fast-sp-dbxr...
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real_DR_embl = Std.dbxref(Std.dbxref_dbname(Martel.Group("data...
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fast_DR_embl = Std.fast_dbxref(real_DR_embl, {"style": "sp-emb...
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DR_embl = Martel.FastFeature(fast_DR_embl, "fast-sp-dbxref", r...
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DR = Martel.Group("DR", Martel.Str("DR ")+ Martel.Group("dat...
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DR_block = sprot38.DR_block
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KW = Simple("KW", "keyword")
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KW_block = Martel.Group("KW_block", Martel.Rep1(KW))
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FT_name = Std.feature_name(Martel.Re(r".{8}"))
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FT_start = Std.feature_location_start(Martel.Re(r".{6}"))
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FT_end = Std.feature_location_end(Martel.Re(r".{6}"))
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FT_desc = Std.feature_description(Martel.UntilEol())
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FT_range = Martel.Str("FT ")+ FT_name+ Martel.Str(" ")+ FT_s...
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FT_continuation = Martel.Str("FT ...
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FT = Std.feature(FT_range+ Martel.Rep(FT_continuation), {"loca...
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feature_block = Std.feature_block(Martel.Rep1(FT), {"style": "...
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SQ = Martel.Group("SQ", Martel.Re("SQ SEQUENCE +(?P<sequence...
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SQ_data = Martel.Str(" ")+ Std.sequence(Martel.UntilEol())...
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sequence = Std.sequence_block(SQ+ Martel.Rep(SQ_data), {"alpha...
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end = Martel.Group("END", Martel.Str("//")+ Martel.AnyEol())
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record = Std.record(ID+ AC_block+ DT_created+ DT_seq_update+ D...
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format_expression = Martel.Group("dataset", Martel.Rep1(record...
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format = Martel.ParseRecords("dataset", {"format": "swissprot/...
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__warningregistry__ = { ( ' Bio.expressions was deprecated, as it ...
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